SentenceTransformer based on cambridgeltl/SapBERT-from-PubMedBERT-fulltext

This is a sentence-transformers model finetuned from cambridgeltl/SapBERT-from-PubMedBERT-fulltext. It maps sentences & paragraphs to a 1536-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.

Model Details

Model Description

Model Type: Sentence Transformer
Base model: cambridgeltl/SapBERT-from-PubMedBERT-fulltext
Maximum Sequence Length: 512 tokens
Output Dimensionality: 1536 dimensions
Similarity Function: Cosine Similarity

Model Sources

Documentation: Sentence Transformers Documentation
Repository: Sentence Transformers on GitHub
Hugging Face: Sentence Transformers on Hugging Face

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': True, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)

Usage

Direct Usage (Sentence Transformers)

First install the Sentence Transformers library:

pip install -U sentence-transformers

Then you can load this model and run inference.

from sentence_transformers import SentenceTransformer

# Download from the 🤗 Hub
model = SentenceTransformer("yyzheng00/sapbert_lora_triplet_rank16")
# Run inference
sentences = [
    '|Product containing tripotassium dicitratobismuthate (medicinal product)| + |Product manufactured as oral dose form (product)| : |Has manufactured dose form (attribute)| = |Oral dose form (dose form)|, { |Has active ingredient (attribute)| = |Tripotassium dicitratobismuthate (substance)| }',
    'Tripotassium dicitratobismuthate in oral dosage form (medicinal product form)',
    'Product containing piracetam in oral dose form (medicinal product form)',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 1536]

# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]

Training Details

Training Dataset

Unnamed Dataset

Size: 800,000 training samples
Columns: sentence_0, sentence_1, and sentence_2

Approximate statistics based on the first 1000 samples:

	sentence_0	sentence_1	sentence_2
type	string	string	string
details	min: 6 tokens mean: 46.56 tokens max: 304 tokens	min: 6 tokens mean: 12.3 tokens max: 33 tokens	min: 6 tokens mean: 20.93 tokens max: 177 tokens

Samples:

sentence_0	sentence_1	sentence_2
`Product containing precisely perindopril erbumine 8 milligram/1 each conventional release oral tablet (clinical drug)`	`Product containing only perindopril erbumine 8 mg/1 each oral tablet (clinical drug)`	`Avascular necrosis of bone of pelvis caused by drug (disorder)`
	Product containing clemastine (medicinal product)	+
	Internal hemorrhoids (disorder)	+

Loss: TripletLoss with these parameters:

{
    "distance_metric": "TripletDistanceMetric.COSINE",
    "triplet_margin": 0.2
}

Training Hyperparameters

Non-Default Hyperparameters

eval_strategy: steps
num_train_epochs: 2
fp16: True
multi_dataset_batch_sampler: round_robin

All Hyperparameters

Click to expand

overwrite_output_dir: False
do_predict: False
eval_strategy: steps
prediction_loss_only: True
per_device_train_batch_size: 8
per_device_eval_batch_size: 8
per_gpu_train_batch_size: None
per_gpu_eval_batch_size: None
gradient_accumulation_steps: 1
eval_accumulation_steps: None
torch_empty_cache_steps: None
learning_rate: 5e-05
weight_decay: 0.0
adam_beta1: 0.9
adam_beta2: 0.999
adam_epsilon: 1e-08
max_grad_norm: 1
num_train_epochs: 2
max_steps: -1
lr_scheduler_type: linear
lr_scheduler_kwargs: {}
warmup_ratio: 0.0
warmup_steps: 0
log_level: passive
log_level_replica: warning
log_on_each_node: True
logging_nan_inf_filter: True
save_safetensors: True
save_on_each_node: False
save_only_model: False
restore_callback_states_from_checkpoint: False
no_cuda: False
use_cpu: False
use_mps_device: False
seed: 42
data_seed: None
jit_mode_eval: False
use_ipex: False
bf16: False
fp16: True
fp16_opt_level: O1
half_precision_backend: auto
bf16_full_eval: False
fp16_full_eval: False
tf32: None
local_rank: 0
ddp_backend: None
tpu_num_cores: None
tpu_metrics_debug: False
debug: []
dataloader_drop_last: False
dataloader_num_workers: 0
dataloader_prefetch_factor: None
past_index: -1
disable_tqdm: False
remove_unused_columns: True
label_names: None
load_best_model_at_end: False
ignore_data_skip: False
fsdp: []
fsdp_min_num_params: 0
fsdp_config: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}
fsdp_transformer_layer_cls_to_wrap: None
accelerator_config: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}
deepspeed: None
label_smoothing_factor: 0.0
optim: adamw_torch
optim_args: None
adafactor: False
group_by_length: False
length_column_name: length
ddp_find_unused_parameters: None
ddp_bucket_cap_mb: None
ddp_broadcast_buffers: False
dataloader_pin_memory: True
dataloader_persistent_workers: False
skip_memory_metrics: True
use_legacy_prediction_loop: False
push_to_hub: False
resume_from_checkpoint: None
hub_model_id: None
hub_strategy: every_save
hub_private_repo: None
hub_always_push: False
gradient_checkpointing: False
gradient_checkpointing_kwargs: None
include_inputs_for_metrics: False
include_for_metrics: []
eval_do_concat_batches: True
fp16_backend: auto
push_to_hub_model_id: None
push_to_hub_organization: None
mp_parameters:
auto_find_batch_size: False
full_determinism: False
torchdynamo: None
ray_scope: last
ddp_timeout: 1800
torch_compile: False
torch_compile_backend: None
torch_compile_mode: None
dispatch_batches: None
split_batches: None
include_tokens_per_second: False
include_num_input_tokens_seen: False
neftune_noise_alpha: None
optim_target_modules: None
batch_eval_metrics: False
eval_on_start: False
use_liger_kernel: False
eval_use_gather_object: False
average_tokens_across_devices: False
prompts: None
batch_sampler: batch_sampler
multi_dataset_batch_sampler: round_robin

Training Logs